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Center for Structural Genomics of Infectious Diseases

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

Mg2+ site A8014 in 1K73 (3.01Å) -- RIBOSOME : Co-crystal structure of anisomycin bound to the 50s ribosomal subunit

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Binding environment of Mg2+ A8014

Site type*

cis-2Oph

Inner
sphere
Oph G:A2102(OP2), G:A2537(OP2)
Or
Ob+Nb
Water A3654, A4160, A7767, A9032
Other
Outer
sphere
Pout
Rout C:A2536, A:A2101
Bout G:A2480, G:A2481, A:A2101
Each outer-sphere moiety is listed only once and only if it does not form inner-sphere interaction
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Inner-sphere Residue Name:
Outer-sphere Moiety Name:
Metal Distances:
Outer-sphere Distances:
B factor(Occupancy):
Nucleic Acid Cartoon:
Spin:
Antialiasing:
On Off
On Off
On Off
On Off
On Off
On Off
On Off
On Off

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].


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